forked from mirrors/nixpkgs
1062 lines
30 KiB
Nix
1062 lines
30 KiB
Nix
/* This file defines the composition for CRAN (R) packages. */
|
|
|
|
{ R, pkgs, overrides }:
|
|
|
|
let
|
|
inherit (pkgs) fetchurl stdenv lib xvfb_run utillinux;
|
|
|
|
buildRPackage = import ./generic-builder.nix { inherit R xvfb_run utillinux ; };
|
|
|
|
# Package template
|
|
#
|
|
# some packages, e.g. cncaGUI, require X running while installation,
|
|
# so that we use xvfb-run if requireX is true.
|
|
derive = lib.makeOverridable ({
|
|
name, version, sha256,
|
|
depends ? [],
|
|
doCheck ? true,
|
|
requireX ? false,
|
|
broken ? false,
|
|
hydraPlatforms ? R.meta.hydraPlatforms
|
|
}: buildRPackage {
|
|
name = "${name}-${version}";
|
|
src = fetchurl {
|
|
urls = [
|
|
"mirror://cran/src/contrib/${name}_${version}.tar.gz"
|
|
"mirror://cran/src/contrib/Archive/${name}/${name}_${version}.tar.gz"
|
|
];
|
|
inherit sha256;
|
|
};
|
|
inherit doCheck requireX;
|
|
propagatedBuildInputs = depends;
|
|
nativeBuildInputs = depends;
|
|
meta.homepage = "http://cran.r-project.org/web/packages/${name}/";
|
|
meta.platforms = R.meta.platforms;
|
|
meta.hydraPlatforms = hydraPlatforms;
|
|
meta.broken = broken;
|
|
});
|
|
|
|
# Overrides package definitions with nativeBuildInputs.
|
|
# For example,
|
|
#
|
|
# overrideNativeBuildInputs {
|
|
# foo = [ pkgs.bar ]
|
|
# } old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.overrideDerivation (attrs: {
|
|
# nativeBuildInputs = attrs.nativeBuildInputs ++ [ pkgs.bar ];
|
|
# });
|
|
# }
|
|
overrideNativeBuildInputs = overrides: old:
|
|
let
|
|
attrNames = builtins.attrNames overrides;
|
|
nameValuePairs = map (name: rec {
|
|
inherit name;
|
|
nativeBuildInputs = builtins.getAttr name overrides;
|
|
value = (builtins.getAttr name old).overrideDerivation (attrs: {
|
|
nativeBuildInputs = attrs.nativeBuildInputs ++ nativeBuildInputs;
|
|
});
|
|
}) attrNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
# Overrides package definitions with buildInputs.
|
|
# For example,
|
|
#
|
|
# overrideBuildInputs {
|
|
# foo = [ pkgs.bar ]
|
|
# } old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.overrideDerivation (attrs: {
|
|
# buildInputs = attrs.buildInputs ++ [ pkgs.bar ];
|
|
# });
|
|
# }
|
|
overrideBuildInputs = overrides: old:
|
|
let
|
|
attrNames = builtins.attrNames overrides;
|
|
nameValuePairs = map (name: rec {
|
|
inherit name;
|
|
buildInputs = builtins.getAttr name overrides;
|
|
value = (builtins.getAttr name old).overrideDerivation (attrs: {
|
|
buildInputs = attrs.buildInputs ++ buildInputs;
|
|
});
|
|
}) attrNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
# Overrides package definition requiring X running to install.
|
|
# For example,
|
|
#
|
|
# overrideRequireX [
|
|
# "foo"
|
|
# ] old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.override {
|
|
# requireX = true;
|
|
# };
|
|
# }
|
|
overrideRequireX = packageNames: old:
|
|
let
|
|
nameValuePairs = map (name: {
|
|
inherit name;
|
|
value = (builtins.getAttr name old).override {
|
|
requireX = true;
|
|
};
|
|
}) packageNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
# Overrides package definition to skip check.
|
|
# For example,
|
|
#
|
|
# overrideSkipCheck [
|
|
# "foo"
|
|
# ] old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.override {
|
|
# doCheck = false;
|
|
# };
|
|
# }
|
|
overrideSkipCheck = packageNames: old:
|
|
let
|
|
nameValuePairs = map (name: {
|
|
inherit name;
|
|
value = (builtins.getAttr name old).override {
|
|
doCheck = false;
|
|
};
|
|
}) packageNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
# Overrides package definition to mark it broken.
|
|
# For example,
|
|
#
|
|
# overrideBroken [
|
|
# "foo"
|
|
# ] old
|
|
#
|
|
# results in
|
|
#
|
|
# {
|
|
# foo = old.foo.override {
|
|
# broken = true;
|
|
# };
|
|
# }
|
|
overrideBroken = packageNames: old:
|
|
let
|
|
nameValuePairs = map (name: {
|
|
inherit name;
|
|
value = (builtins.getAttr name old).override {
|
|
broken = true;
|
|
};
|
|
}) packageNames;
|
|
in
|
|
builtins.listToAttrs nameValuePairs;
|
|
|
|
defaultOverrides = old: new:
|
|
let old0 = old; in
|
|
let
|
|
old1 = old0 // (overrideRequireX packagesRequireingX old0);
|
|
old2 = old1 // (overrideSkipCheck packagesToSkipCheck old1);
|
|
old3 = old2 // (overrideNativeBuildInputs packagesWithNativeBuildInputs old2);
|
|
old4 = old3 // (overrideBuildInputs packagesWithBuildInputs old3);
|
|
old5 = old4 // (overrideBroken brokenPackages old4);
|
|
old = old5;
|
|
in old // (otherOverrides old new);
|
|
|
|
# Recursive override pattern.
|
|
# `_self` is a collection of packages;
|
|
# `self` is `_self` with overridden packages;
|
|
# packages in `_self` may depends on overridden packages.
|
|
self = (defaultOverrides _self self) // overrides;
|
|
_self = import ./cran-packages.nix { inherit self derive; };
|
|
|
|
# tweaks for the individual packages and "in self" follow
|
|
|
|
packagesWithNativeBuildInputs = {
|
|
# sort -t '=' -k 2
|
|
RAppArmor = [ pkgs.apparmor ];
|
|
SOD = [ pkgs.cudatoolkit ]; # requres CL/cl.h
|
|
curl = [ pkgs.curl pkgs.openldap ];
|
|
Rssa = [ pkgs.fftw ];
|
|
fftw = [ pkgs.fftw ];
|
|
fftwtools = [ pkgs.fftw ];
|
|
kza = [ pkgs.fftw ];
|
|
mwaved = [ pkgs.fftw ];
|
|
spate = [ pkgs.fftw ];
|
|
chebpol = [ pkgs.fftw ];
|
|
seewave = [ pkgs.fftw pkgs.libsndfile ];
|
|
rgeos = [ pkgs.geos ];
|
|
Rglpk = [ pkgs.glpk ];
|
|
RCA = [ pkgs.gmp ];
|
|
gmp = [ pkgs.gmp ];
|
|
rcdd = [ pkgs.gmp ];
|
|
igraph = [ pkgs.gmp ];
|
|
glpkAPI = [ pkgs.gmp pkgs.glpk ];
|
|
sdcTable = [ pkgs.gmp pkgs.glpk ];
|
|
Rmpfr = [ pkgs.gmp pkgs.mpfr ];
|
|
BNSP = [ pkgs.gsl ];
|
|
BayesSAE = [ pkgs.gsl ];
|
|
BayesVarSel = [ pkgs.gsl ];
|
|
HiCseg = [ pkgs.gsl ];
|
|
KFKSDS = [ pkgs.gsl ];
|
|
R2GUESS = [ pkgs.gsl ];
|
|
RcppZiggurat = [ pkgs.gsl ];
|
|
SemiCompRisks = [ pkgs.gsl ];
|
|
VBLPCM = [ pkgs.gsl ];
|
|
abn = [ pkgs.gsl ];
|
|
cit = [ pkgs.gsl ];
|
|
libamtrack = [ pkgs.gsl ];
|
|
mixcat = [ pkgs.gsl ];
|
|
outbreaker = [ pkgs.gsl ];
|
|
ridge = [ pkgs.gsl ];
|
|
simplexreg = [ pkgs.gsl ];
|
|
stsm = [ pkgs.gsl ];
|
|
survSNP = [ pkgs.gsl ];
|
|
topicmodels = [ pkgs.gsl ];
|
|
RcppGSL = [ pkgs.gsl ];
|
|
bnpmr = [ pkgs.gsl ];
|
|
geoCount = [ pkgs.gsl ];
|
|
gsl = [ pkgs.gsl ];
|
|
mvabund = [ pkgs.gsl ];
|
|
diversitree = [ pkgs.gsl pkgs.fftw ];
|
|
VBmix = [ pkgs.gsl pkgs.fftw pkgs.qt4 ];
|
|
RGtk2 = [ pkgs.gtk2 ];
|
|
cairoDevice = [ pkgs.gtk2 ];
|
|
adimpro = [ pkgs.imagemagick ];
|
|
rjags = [ pkgs.jags ];
|
|
runjags = [ pkgs.jags ];
|
|
JavaGD = [ pkgs.jdk ];
|
|
RODBC = [ pkgs.libiodbc ];
|
|
RODBCext = [ pkgs.libiodbc ];
|
|
jpeg = [ pkgs.libjpeg ];
|
|
EMCluster = [ pkgs.liblapack ];
|
|
png = [ pkgs.libpng ];
|
|
rtiff = [ pkgs.libtiff ];
|
|
tiff = [ pkgs.libtiff ];
|
|
Cairo = [ pkgs.libtiff pkgs.libjpeg pkgs.cairo ];
|
|
XML = [ pkgs.libtool pkgs.libxml2 pkgs.xmlsec pkgs.libxslt ];
|
|
rpud = [ pkgs.linuxPackages.nvidia_x11 ];
|
|
CARramps = [ pkgs.linuxPackages.nvidia_x11 pkgs.liblapack ];
|
|
rgl = [ pkgs.mesa pkgs.x11 ];
|
|
ncdf = [ pkgs.netcdf ];
|
|
ncdf4 = [ pkgs.netcdf ];
|
|
pbdNCDF4 = [ pkgs.netcdf ];
|
|
RNetCDF = [ pkgs.netcdf pkgs.udunits ];
|
|
nloptr = [ pkgs.nlopt ];
|
|
npRmpi = [ pkgs.openmpi ];
|
|
pbdPROF = [ pkgs.openmpi ];
|
|
sprint = [ pkgs.openmpi ];
|
|
Rmpi = [ pkgs.openmpi ];
|
|
openssl = [ pkgs.openssl ];
|
|
PKI = [ pkgs.openssl ];
|
|
RSclient = [ pkgs.openssl ];
|
|
Rserve = [ pkgs.openssl ];
|
|
Rpoppler = [ pkgs.poppler ];
|
|
audio = [ pkgs.portaudio ];
|
|
rpg = [ pkgs.postgresql ];
|
|
RPostgreSQL = [ pkgs.postgresql ];
|
|
ssanv = [ pkgs.proj ];
|
|
proj4 = [ pkgs.proj ];
|
|
rgdal = [ pkgs.proj pkgs.gdal ];
|
|
RProtoBuf = [ pkgs.protobuf ];
|
|
rPython = [ pkgs.python ];
|
|
qtpaint = [ pkgs.qt4 ];
|
|
qtbase = [ pkgs.qt4 ];
|
|
BayesXsrc = [ pkgs.readline pkgs.ncurses ];
|
|
udunits2 = [ pkgs.udunits pkgs.expat ];
|
|
tkrplot = [ pkgs.xlibs.libX11 ];
|
|
rzmq = [ pkgs.zeromq2 ];
|
|
PopGenome = [ pkgs.zlib ];
|
|
RJaCGH = [ pkgs.zlib ];
|
|
RcppCNPy = [ pkgs.zlib ];
|
|
rbamtools = [ pkgs.zlib ];
|
|
rmatio = [ pkgs.zlib ];
|
|
RVowpalWabbit = [ pkgs.zlib pkgs.boost ];
|
|
seqminer = [ pkgs.zlib pkgs.bzip2 ];
|
|
rphast = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
|
|
rtfbs = [ pkgs.zlib pkgs.bzip2 pkgs.gzip pkgs.readline ];
|
|
Rhpc = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.openmpi pkgs.pcre ];
|
|
SAVE = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre ];
|
|
RcppOctave = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.octave ];
|
|
rJava = [ pkgs.zlib pkgs.bzip2 pkgs.icu pkgs.lzma pkgs.pcre pkgs.jdk pkgs.libzip ];
|
|
R2SWF = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
|
|
sysfonts = [ pkgs.zlib pkgs.libpng pkgs.freetype ];
|
|
showtext = [ pkgs.zlib pkgs.libpng pkgs.icu pkgs.freetype ];
|
|
XBRL = [ pkgs.zlib pkgs.libxml2 ];
|
|
RMySQL = [ pkgs.zlib pkgs.mysql ];
|
|
};
|
|
|
|
packagesWithBuildInputs = {
|
|
# sort -t '=' -k 2
|
|
qtpaint = [ pkgs.cmake ];
|
|
qtbase = [ pkgs.cmake pkgs.perl ];
|
|
gmatrix = [ pkgs.cudatoolkit ];
|
|
WideLM = [ pkgs.cudatoolkit ];
|
|
RCurl = [ pkgs.curl ];
|
|
R2SWF = [ pkgs.pkgconfig ];
|
|
RGtk2 = [ pkgs.pkgconfig ];
|
|
RProtoBuf = [ pkgs.pkgconfig ];
|
|
Rpoppler = [ pkgs.pkgconfig ];
|
|
VBmix = [ pkgs.pkgconfig ];
|
|
XML = [ pkgs.pkgconfig ];
|
|
cairoDevice = [ pkgs.pkgconfig ];
|
|
chebpol = [ pkgs.pkgconfig ];
|
|
fftw = [ pkgs.pkgconfig ];
|
|
geoCount = [ pkgs.pkgconfig ];
|
|
kza = [ pkgs.pkgconfig ];
|
|
mwaved = [ pkgs.pkgconfig ];
|
|
showtext = [ pkgs.pkgconfig ];
|
|
spate = [ pkgs.pkgconfig ];
|
|
stringi = [ pkgs.pkgconfig ];
|
|
sysfonts = [ pkgs.pkgconfig ];
|
|
Cairo = [ pkgs.pkgconfig ];
|
|
Rsymphony = [ pkgs.pkgconfig pkgs.doxygen pkgs.graphviz pkgs.subversion ];
|
|
qtutils = [ pkgs.qt4 ];
|
|
tcltk2 = [ pkgs.tcl pkgs.tk ];
|
|
tikzDevice = [ pkgs.texLive ];
|
|
rPython = [ pkgs.which ];
|
|
CARramps = [ pkgs.which pkgs.cudatoolkit ];
|
|
gputools = [ pkgs.which pkgs.cudatoolkit ];
|
|
rpud = [ pkgs.which pkgs.cudatoolkit ];
|
|
adimpro = [ pkgs.which pkgs.xorg.xdpyinfo ];
|
|
PET = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
|
|
dti = [ pkgs.which pkgs.xorg.xdpyinfo pkgs.imagemagick ];
|
|
};
|
|
|
|
packagesRequireingX = [
|
|
"AnalyzeFMRI"
|
|
"AnnotLists"
|
|
"AnthropMMD"
|
|
"AtelieR"
|
|
"BAT"
|
|
"BCA"
|
|
"BEQI2"
|
|
"BHMSMAfMRI"
|
|
"BioGeoBEARS"
|
|
"BiodiversityR"
|
|
"CCTpack"
|
|
"CommunityCorrelogram"
|
|
"ConvergenceConcepts"
|
|
"DALY"
|
|
"DSpat"
|
|
"Deducer"
|
|
"DeducerExtras"
|
|
"DeducerPlugInExample"
|
|
"DeducerPlugInScaling"
|
|
"DeducerSpatial"
|
|
"DeducerSurvival"
|
|
"DeducerText"
|
|
"Demerelate"
|
|
"DescTools"
|
|
"DivMelt"
|
|
"ENiRG"
|
|
"EcoVirtual"
|
|
"EnQuireR"
|
|
"FAiR"
|
|
"FD"
|
|
"FFD"
|
|
"FeedbackTS"
|
|
"FreeSortR"
|
|
"GGEBiplotGUI"
|
|
"GPCSIV"
|
|
"GUniFrac"
|
|
"Geneland"
|
|
"GeoGenetix"
|
|
"GeoXp"
|
|
"GrammR"
|
|
"GrapheR"
|
|
"GroupSeq"
|
|
"HH"
|
|
"HiveR"
|
|
"IsotopeR"
|
|
"JGR"
|
|
"KappaGUI"
|
|
"LS2Wstat"
|
|
"MAR1"
|
|
"MTurkR"
|
|
"MareyMap"
|
|
"MergeGUI"
|
|
"Meth27QC"
|
|
"MicroStrategyR"
|
|
"MissingDataGUI"
|
|
"MplusAutomation"
|
|
"OligoSpecificitySystem"
|
|
"OpenRepGrid"
|
|
"PBSadmb"
|
|
"PBSmodelling"
|
|
"PCPS"
|
|
"PopGenReport"
|
|
"PredictABEL"
|
|
"PrevMap"
|
|
"ProbForecastGOP"
|
|
"QCAGUI"
|
|
"R2STATS"
|
|
"RHRV"
|
|
"RNCEP"
|
|
"RQDA"
|
|
"RSDA"
|
|
"RSurvey"
|
|
"RandomFields"
|
|
"Rcmdr"
|
|
"RcmdrPlugin_BCA"
|
|
"RcmdrPlugin_DoE"
|
|
"RcmdrPlugin_EACSPIR"
|
|
"RcmdrPlugin_EBM"
|
|
"RcmdrPlugin_EZR"
|
|
"RcmdrPlugin_EcoVirtual"
|
|
"RcmdrPlugin_FactoMineR"
|
|
"RcmdrPlugin_HH"
|
|
"RcmdrPlugin_IPSUR"
|
|
"RcmdrPlugin_KMggplot2"
|
|
"RcmdrPlugin_MA"
|
|
"RcmdrPlugin_MPAStats"
|
|
"RcmdrPlugin_ROC"
|
|
"RcmdrPlugin_SCDA"
|
|
"RcmdrPlugin_SLC"
|
|
"RcmdrPlugin_SM"
|
|
"RcmdrPlugin_StatisticalURV"
|
|
"RcmdrPlugin_TeachingDemos"
|
|
"RcmdrPlugin_UCA"
|
|
"RcmdrPlugin_coin"
|
|
"RcmdrPlugin_depthTools"
|
|
"RcmdrPlugin_doex"
|
|
"RcmdrPlugin_epack"
|
|
"RcmdrPlugin_lfstat"
|
|
"RcmdrPlugin_mosaic"
|
|
"RcmdrPlugin_orloca"
|
|
"RcmdrPlugin_plotByGroup"
|
|
"RcmdrPlugin_pointG"
|
|
"RcmdrPlugin_qual"
|
|
"RcmdrPlugin_sampling"
|
|
"RcmdrPlugin_sos"
|
|
"RcmdrPlugin_steepness"
|
|
"RcmdrPlugin_survival"
|
|
"RcmdrPlugin_temis"
|
|
"RenextGUI"
|
|
"RunuranGUI"
|
|
"SOLOMON"
|
|
"SPACECAP"
|
|
"SRRS"
|
|
"SSDforR"
|
|
"STEPCAM"
|
|
"SYNCSA"
|
|
"Simile"
|
|
"SimpleTable"
|
|
"StatDA"
|
|
"SyNet"
|
|
"TDMR"
|
|
"TED"
|
|
"TIMP"
|
|
"TTAinterfaceTrendAnalysis"
|
|
"TestScorer"
|
|
"VIMGUI"
|
|
"VecStatGraphs3D"
|
|
"WMCapacity"
|
|
"accrual"
|
|
"ade4TkGUI"
|
|
"adehabitat"
|
|
"analogue"
|
|
"analogueExtra"
|
|
"aplpack"
|
|
"aqfig"
|
|
"arf3DS4"
|
|
"asbio"
|
|
"bayesDem"
|
|
"betapart"
|
|
"betaper"
|
|
"bio_infer"
|
|
"bipartite"
|
|
"biplotbootGUI"
|
|
"blender"
|
|
"cairoDevice"
|
|
"cncaGUI"
|
|
"cocorresp"
|
|
"confidence"
|
|
"constrainedKriging"
|
|
"cpa"
|
|
"dave"
|
|
"debug"
|
|
"detrendeR"
|
|
"dgmb"
|
|
"dpa"
|
|
"dynBiplotGUI"
|
|
"dynamicGraph"
|
|
"eVenn"
|
|
"exactLoglinTest"
|
|
"fSRM"
|
|
"fat2Lpoly"
|
|
"fbati"
|
|
"feature"
|
|
"fgui"
|
|
"fisheyeR"
|
|
"fit4NM"
|
|
"forams"
|
|
"forensim"
|
|
"fscaret"
|
|
"gWidgets2RGtk2"
|
|
"gWidgets2tcltk"
|
|
"gWidgetsRGtk2"
|
|
"gWidgetstcltk"
|
|
"gcmr"
|
|
"geoR"
|
|
"geoRglm"
|
|
"geomorph"
|
|
"georob"
|
|
"gnm"
|
|
"gsubfn"
|
|
"iBUGS"
|
|
"iDynoR"
|
|
"ic50"
|
|
"in2extRemes"
|
|
"iplots"
|
|
"isopam"
|
|
"likeLTD"
|
|
"loe"
|
|
"logmult"
|
|
"memgene"
|
|
"metacom"
|
|
"migui"
|
|
"miniGUI"
|
|
"mixsep"
|
|
"mlDNA"
|
|
"mpmcorrelogram"
|
|
"mritc"
|
|
"multgee"
|
|
"multibiplotGUI"
|
|
"nodiv"
|
|
"onemap"
|
|
"palaeoSig"
|
|
"paleoMAS"
|
|
"pbatR"
|
|
"pez"
|
|
"phylotools"
|
|
"picante"
|
|
"playwith"
|
|
"plotSEMM"
|
|
"plsRbeta"
|
|
"plsRglm"
|
|
"pmg"
|
|
"poppr"
|
|
"powerpkg"
|
|
"prefmod"
|
|
"qtbase"
|
|
"qtpaint"
|
|
"qtutils"
|
|
"r4ss"
|
|
"rAverage"
|
|
"rareNMtests"
|
|
"recluster"
|
|
"relax"
|
|
"relimp"
|
|
"reportRx"
|
|
"reshapeGUI"
|
|
"rgl"
|
|
"rich"
|
|
"ringscale"
|
|
"rioja"
|
|
"ripa"
|
|
"rite"
|
|
"rnbn"
|
|
"rriskDistributions"
|
|
"rsgcc"
|
|
"sdcMicroGUI"
|
|
"sharpshootR"
|
|
"simba"
|
|
"soundecology"
|
|
"spacodiR"
|
|
"spatsurv"
|
|
"sqldf"
|
|
"statcheck"
|
|
"stosim"
|
|
"strvalidator"
|
|
"stylo"
|
|
"svDialogstcltk"
|
|
"svIDE"
|
|
"svSocket"
|
|
"svWidgets"
|
|
"tcltk2"
|
|
"titan"
|
|
"tkrgl"
|
|
"tkrplot"
|
|
"tmap"
|
|
"tspmeta"
|
|
"twiddler"
|
|
"vcdExtra"
|
|
"vegan"
|
|
"vegan3d"
|
|
"vegclust"
|
|
"x12GUI"
|
|
"xergm"
|
|
];
|
|
|
|
packagesToSkipCheck = [
|
|
"Rmpi" # tries to run MPI processes
|
|
"gmatrix" # requires CUDA runtime
|
|
"npRmpi" # tries to run MPI processes
|
|
"sprint" # tries to run MPI processes
|
|
];
|
|
|
|
# Packages which cannot be installed due to lack of dependencies or other reasons.
|
|
brokenPackages = [ # sort -t '#' -k 2
|
|
"metabolomics" # depends on broken crmn
|
|
"retistruct" # depends on broken RImageJROI
|
|
"CARrampsOcl" # depends on OpenCL
|
|
"rpanel" # I could not make Tcl to recognize BWidget. HELP WANTED!
|
|
"alm" # jsonlite.so: undefined symbol: XXX
|
|
"archivist" # jsonlite.so: undefined symbol: XXX
|
|
"bold" # jsonlite.so: undefined symbol: XXX
|
|
"enigma" # jsonlite.so: undefined symbol: XXX
|
|
"exCon" # jsonlite.so: undefined symbol: XXX
|
|
"gender" # jsonlite.so: undefined symbol: XXX
|
|
"jSonarR" # jsonlite.so: undefined symbol: XXX
|
|
"leafletR" # jsonlite.so: undefined symbol: XXX
|
|
"opencpu" # jsonlite.so: undefined symbol: XXX
|
|
"pdfetch" # jsonlite.so: undefined symbol: XXX
|
|
"polidata" # jsonlite.so: undefined symbol: XXX
|
|
"pollstR" # jsonlite.so: undefined symbol: XXX
|
|
"rbison" # jsonlite.so: undefined symbol: XXX
|
|
"RGA" # jsonlite.so: undefined symbol: XXX
|
|
"rHealthDataGov" # jsonlite.so: undefined symbol: XXX
|
|
"rinat" # jsonlite.so: undefined symbol: XXX
|
|
"rjstat" # jsonlite.so: undefined symbol: XXX
|
|
"rmongodb" # jsonlite.so: undefined symbol: XXX
|
|
"rnoaa" # jsonlite.so: undefined symbol: XXX
|
|
"RSiteCatalyst" # jsonlite.so: undefined symbol: XXX
|
|
"rsunlight" # jsonlite.so: undefined symbol: XXX
|
|
"rWBclimate" # jsonlite.so: undefined symbol: XXX
|
|
"SGP" # jsonlite.so: undefined symbol: XXX
|
|
"slackr" # jsonlite.so: undefined symbol: XXX
|
|
"SocialMediaMineR" # jsonlite.so: undefined symbol: XXX
|
|
"webutils" # jsonlite.so: undefined symbol: XXX
|
|
"WikipediR" # jsonlite.so: undefined symbol: XXX
|
|
"demi" # requires affy, affxparser, and oligo
|
|
"KANT" # requires affy, and Biobase
|
|
"pathClass" # requires affy, and Biobase
|
|
"msarc" # requires AnnotationDbi
|
|
"ACNE" # requires aroma_affymetrix
|
|
"aroma_affymetrix" # requires aroma_core
|
|
"calmate" # requires aroma_core
|
|
"NSA" # requires aroma_core
|
|
"beadarrayFilter" # requires beadarray
|
|
"compendiumdb" # requires Biobase
|
|
"ktspair" # requires Biobase
|
|
"MetaLandSim" # requires Biobase
|
|
"permGPU" # requires Biobase
|
|
"propOverlap" # requires Biobase
|
|
"RobLoxBioC" # requires Biobase
|
|
"RobLox" # requires Biobase
|
|
"IsoGene" # requires Biobase, and affy
|
|
"mGSZ" # requires Biobase, and limma
|
|
"GExMap" # requires Biobase and multtest
|
|
"netweavers" # requires BiocGenerics, Biobase, and limma
|
|
"NCmisc" # requires BiocInstaller
|
|
"EMDomics" # requires BiocParallel
|
|
"PepPrep" # requires biomaRt
|
|
"snplist" # requires biomaRt
|
|
"ionflows" # requires Biostrings
|
|
"RADami" # requires Biostrings
|
|
"SimRAD" # requires Biostrings, and ShortRead
|
|
"SeqFeatR" # requires Biostrings, qvalue, and widgetTools
|
|
"RAPIDR" # requires Biostrings, Rsamtools, and GenomicRanges
|
|
"FunctionalNetworks" # requires breastCancerVDX, and Biobase
|
|
"rJPSGCS" # requires chopsticks
|
|
"OpenCL" # requires CL/opencl.h
|
|
"clpAPI" # requires clp
|
|
"pcaL1" # requires clp
|
|
"bmrm" # requires clpAPI
|
|
"sequenza" # requires copynumber
|
|
"cplexAPI" # requires CPLEX
|
|
"Rcplex" # requires cplexAPI
|
|
"empiricalFDR_DESeq2" # requires DESeq2, and GenomicRanges
|
|
"CHAT" # requires DNAcopy
|
|
"ParDNAcopy" # requires DNAcopy
|
|
"PSCBS" # requires DNAcopy
|
|
"dcGOR" # requires dnet
|
|
"bcool" # requires doMPI
|
|
"gitter" # requires EBImage
|
|
"Rcell" # requires EBImage
|
|
"RockFab" # requires EBImage
|
|
"babel" # requires edgeR
|
|
"edgeRun" # requires edgeR
|
|
"GSAgm" # requires edgeR
|
|
"HTSCluster" # requires edgeR
|
|
"QuasiSeq" # requires edgeR
|
|
"SimSeq" # requires edgeR
|
|
"BcDiag" # requires fabia
|
|
"superbiclust" # requires fabia
|
|
"curvHDR" # requires flowCore
|
|
"RbioRXN" # requires fmcsR, and KEGGREST
|
|
"qdap" # requires gender
|
|
"orQA" # requires genefilter
|
|
"apmsWAPP" # requires genefilter, Biobase, multtest, edgeR, DESeq, and aroma.light
|
|
"ExomeDepth" # requires GenomicRanges, and Rsamtools
|
|
"rggobi" # requires GGobi
|
|
"miRtest" # requires globaltest, GlobalAncova, and limma
|
|
"PANDA" # requires GO.db
|
|
"BiSEp" # requires GOSemSim, GO.db, and org.Hs.eg.db
|
|
"PubMedWordcloud" # requires GOsummaries
|
|
"eulerian" # requires graph
|
|
"gRapHD" # requires graph
|
|
"msSurv" # requires graph
|
|
"PairViz" # requires graph
|
|
"iRefR" # requires graph, and RBGL
|
|
"pcalg" # requires graph, and RBGL
|
|
"protiq" # requires graph, and RBGL
|
|
"RnavGraph" # requires graph, and RBGL
|
|
"classGraph" # requires graph, and Rgraphviz
|
|
"epoc" # requires graph, and Rgraphviz
|
|
"gridGraphviz" # requires graph, and Rgraphviz
|
|
"QuACN" # requires graph, RBGL
|
|
"D2C" # requires gRbase
|
|
"gRain" # requires gRbase
|
|
"gRc" # requires gRbase
|
|
"gRim" # requires gRbase
|
|
"LogisticDx" # requires gRbase
|
|
"topologyGSA" # requires gRbase
|
|
"gridDebug" # requires gridGraphviz
|
|
"RAM" # requires Heatplus
|
|
"RcppRedis" # requires Hiredis
|
|
"HTSDiff" # requires HTSCluster
|
|
"interval" # requires Icens
|
|
"FAMT" # requires impute
|
|
"moduleColor" # requires impute
|
|
"PMA" # requires impute
|
|
"samr" # requires impute
|
|
"swamp" # requires impute
|
|
"WGCNA" # requires impute
|
|
"MetaDE" # requires impute, and Biobase
|
|
"FHtest" # requires interval
|
|
"MSIseq" # requires IRanges
|
|
"SNPtools" # requires IRanges, GenomicRanges, Biostrings, and Rsamtools
|
|
"RefFreeEWAS" # requires isva
|
|
"PhViD" # requires LBE
|
|
"AntWeb" # requires leafletR
|
|
"ecoengine" # requires leafletR
|
|
"spocc" # requires leafletR
|
|
"RDieHarder" # requires libdieharder
|
|
"sybilSBML" # requires libSBML
|
|
"CORM" # requires limma
|
|
"DAAGbio" # requires limma
|
|
"DCGL" # requires limma
|
|
"metaMA" # requires limma
|
|
"plmDE" # requires limma
|
|
"SQDA" # requires limma
|
|
"PerfMeas" # requires limma, graph, and RBGL
|
|
"rLindo" # requires LINDO API
|
|
"magma" # requires MAGMA
|
|
"HiPLARM" # requires MAGMA or PLASMA
|
|
"MAMA" # requires metaMA
|
|
"Rmosek" # requires mosek
|
|
"bigGP" # requires MPI running. HELP WANTED!
|
|
"doMPI" # requires MPI running. HELP WANTED!
|
|
"metaMix" # requires MPI running. HELP WANTED!
|
|
"pbdMPI" # requires MPI running. HELP WANTED!
|
|
"pmclust" # requires MPI running. HELP WANTED!
|
|
"MSeasyTkGUI" # requires MSeasyTkGUI
|
|
"hddplot" # requires multtest
|
|
"mutoss" # requires multtest
|
|
"PCS" # requires multtest
|
|
"structSSI" # requires multtest
|
|
"TcGSA" # requires multtest
|
|
"mutossGUI" # requires mutoss
|
|
"Biograph" # requires mvna
|
|
"MSeasy" # requires mzR, and xcms
|
|
"bigpca" # requires NCmisc
|
|
"reader" # requires NCmisc
|
|
"ROracle" # requires OCI
|
|
"BRugs" # requires OpenBUGS
|
|
"x_ent" # requires opencpu
|
|
"pbdBASE" # requires pbdMPI
|
|
"pbdDEMO" # requires pbdMPI
|
|
"pbdDMAT" # requires pbdMPI
|
|
"pbdSLAP" # requires pbdMPI
|
|
"qtlnet" # requires pcalg
|
|
"agridat" # requires pcaMethods
|
|
"LOST" # requires pcaMethods
|
|
"multiDimBio" # requires pcaMethods
|
|
"crmn" # requires pcaMethods, and Biobase
|
|
"imputeLCMD" # requires pcaMethods, and impute
|
|
"MEET" # requires pcaMethods, and seqLogo
|
|
"saps" # requires piano, and survcomp
|
|
"smart" # requires PMA
|
|
"surveillance" # requires polyCub
|
|
"aLFQ" # requires protiq
|
|
"aroma_cn" # requires PSCBS
|
|
"aroma_core" # requires PSCBS
|
|
"NLPutils" # requires qdap
|
|
"RQuantLib" # requires QuantLib
|
|
"evora" # requires qvalue
|
|
"isva" # requires qvalue
|
|
"NBPSeq" # requires qvalue
|
|
"pi0" # requires qvalue
|
|
"RSNPset" # requires qvalue
|
|
"gRbase" # requires RBGL, and graph
|
|
"RSeed" # requires RBGL, and graph
|
|
"beadarrayMSV" # requires rggobi
|
|
"clusterfly" # requires rggobi
|
|
"PKgraph" # requires rggobi
|
|
"SeqGrapheR" # requires rggobi
|
|
"branchLars" # requires Rgraphviz
|
|
"hasseDiagram" # requires Rgraphviz
|
|
"hpoPlot" # requires Rgraphviz
|
|
"strum" # requires Rgraphviz
|
|
"CrypticIBDcheck" # requires rJPSGCS
|
|
"dagbag" # requires Rlapack
|
|
"ltsk" # requires Rlapack and Rblas
|
|
"cqrReg" # requires Rmosek
|
|
"REBayes" # requires Rmosek
|
|
"fPortfolio" # requires rneos
|
|
"HierO" # requires rneos
|
|
"ora" # requires ROracle
|
|
"biotools" # requires rpanel
|
|
"erpR" # requires rpanel
|
|
"gamlss_demo" # requires rpanel
|
|
"GUIDE" # requires rpanel
|
|
"lgcp" # requires rpanel
|
|
"optBiomarker" # requires rpanel
|
|
"SDD" # requires rpanel
|
|
"soilphysics" # requires rpanel
|
|
"vows" # requires rpanel
|
|
"LinRegInteractive" # requires Rpanel
|
|
"RVideoPoker" # requires Rpanel
|
|
"semiArtificial" # requires RSNNS
|
|
"PCGSE" # requires safe
|
|
"ArrayBin" # requires SAGx
|
|
"DepthProc" # requires samr
|
|
"netClass" # requires samr
|
|
"RSAP" # requires SAPNWRFCSDK
|
|
"DBKGrad" # requires SDD
|
|
"RcmdrPlugin_seeg" # requires seeg
|
|
"EMA" # requires siggenes, affy, multtest, gcrma, biomaRt, and AnnotationDbi
|
|
"GeneticTools" # requires snpStats
|
|
"snpEnrichment" # requires snpStats
|
|
"snpStatsWriter" # requires snpStats
|
|
"wgsea" # requires snpStats
|
|
"rysgran" # requires soiltexture
|
|
"adaptsmoFMRI" # requires spatstat
|
|
"ads" # requires spatstat
|
|
"aoristic" # requires spatstat
|
|
"dbmss" # requires spatstat
|
|
"Digiroo2" # requires spatstat
|
|
"dixon" # requires spatstat
|
|
"dpcR" # requires spatstat
|
|
"DSpat" # requires spatstat
|
|
"ecespa" # requires spatstat
|
|
"ecospat" # requires spatstat
|
|
"ETAS" # requires spatstat
|
|
"GriegSmith" # requires spatstat
|
|
"intamapInteractive" # requires spatstat
|
|
"latticeDensity" # requires spatstat
|
|
"polyCub" # requires spatstat
|
|
"RImageJROI" # requires spatstat
|
|
"seeg" # requires spatstat
|
|
"SGCS" # requires spatstat
|
|
"siar" # requires spatstat
|
|
"siplab" # requires spatstat
|
|
"sparr" # requires spatstat
|
|
"spatialsegregation" # requires spatstat
|
|
"SpatialVx" # requires spatstat
|
|
"stpp" # requires spatstat
|
|
"trip" # requires spatstat
|
|
"pubmed_mineR" # requires SSOAP
|
|
"dnet" # requires supraHex, graph, Rgraphviz, and Biobase
|
|
"plsRcox" # requires survcomp
|
|
"rsig" # requires survcomp
|
|
"leapp" # requires sva
|
|
"ttScreening" # requires sva, and limma
|
|
"GOGANPA" # requires WGCNA
|
|
"nettools" # requires WGCNA
|
|
"rneos" # requires XMLRPC
|
|
"taxize" # requres bold
|
|
"cudaBayesreg" # requres Rmath
|
|
"rsprng" # requres sprng
|
|
"evobiR" # requres taxiz
|
|
"bdvis" # requres taxize
|
|
"RNeXML" # requres taxize
|
|
"TR8" # requres taxize
|
|
"Actigraphy" # SDMTools.so: undefined symbol: X
|
|
"lefse" # SDMTools.so: undefined symbol: X
|
|
"raincpc" # SDMTools.so: undefined symbol: X
|
|
"rainfreq" # SDMTools.so: undefined symbol: X
|
|
"MigClim" # SDMTools.So: Undefined Symbol: X
|
|
"PatternClass" # SDMTools.So: Undefined Symbol: X
|
|
"qtbase" # the smokegen binary cannot find libQtCore.so.4 etc. at runtime
|
|
"jvmr" # tries to download files during its build
|
|
"h2o" # tries to download some h2o.jar during its build
|
|
];
|
|
|
|
otherOverrides = old: new: {
|
|
curl = old.curl.overrideDerivation (attrs: {
|
|
preConfigure = "export CURL_INCLUDES=${pkgs.curl}/include/curl";
|
|
});
|
|
|
|
RcppArmadillo = old.RcppArmadillo.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
rpf = old.rpf.overrideDerivation (attrs: {
|
|
patchPhase = "patchShebangs configure";
|
|
});
|
|
|
|
BayesXsrc = old.BayesXsrc.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesXsrc.patch ];
|
|
});
|
|
|
|
rJava = old.rJava.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
JavaGD = old.JavaGD.overrideDerivation (attrs: {
|
|
preConfigure = ''
|
|
export JAVA_CPPFLAGS=-I${pkgs.jdk}/include/
|
|
export JAVA_HOME=${pkgs.jdk}
|
|
'';
|
|
});
|
|
|
|
Mposterior = old.Mposterior.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
|
});
|
|
|
|
qtbase = old.qtbase.overrideDerivation (attrs: {
|
|
patches = [ ./patches/qtbase.patch ];
|
|
});
|
|
|
|
Rmpi = old.Rmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
npRmpi = old.npRmpi.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-Rmpi-type=OPENMPI"
|
|
];
|
|
});
|
|
|
|
Rmpfr = old.Rmpfr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mpfr-include=${pkgs.mpfr}/include"
|
|
];
|
|
});
|
|
|
|
RVowpalWabbit = old.RVowpalWabbit.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-boost=${pkgs.boost.dev}" "--with-boost-libdir=${pkgs.boost.lib}/lib"
|
|
];
|
|
});
|
|
|
|
RAppArmor = old.RAppArmor.overrideDerivation (attrs: {
|
|
patches = [ ./patches/RAppArmor.patch ];
|
|
LIBAPPARMOR_HOME = "${pkgs.apparmor}";
|
|
});
|
|
|
|
RMySQL = old.RMySQL.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-mysql-dir=${pkgs.mysql}"
|
|
];
|
|
});
|
|
|
|
slfm = old.slfm.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
|
});
|
|
|
|
SamplerCompare = old.SamplerCompare.overrideDerivation (attrs: {
|
|
PKG_LIBS = "-L${pkgs.atlas}/lib -lf77blas -latlas";
|
|
});
|
|
|
|
gputools = old.gputools.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gputools.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
# It seems that we cannot override meta attributes with overrideDerivation.
|
|
CARramps = (old.CARramps.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
|
|
patches = [ ./patches/CARramps.patch ];
|
|
configureFlags = [
|
|
"--with-cuda-home=${pkgs.cudatoolkit}"
|
|
];
|
|
});
|
|
|
|
gmatrix = old.gmatrix.overrideDerivation (attrs: {
|
|
patches = [ ./patches/gmatrix.patch ];
|
|
CUDA_LIB_PATH = "${pkgs.cudatoolkit}/lib64";
|
|
R_INC_PATH = "${pkgs.R}/lib/R/include";
|
|
CUDA_INC_PATH = "${pkgs.cudatoolkit}/usr_include";
|
|
});
|
|
|
|
# It seems that we cannot override meta attributes with overrideDerivation.
|
|
rpud = (old.rpud.override { hydraPlatforms = stdenv.lib.platforms.none; }).overrideDerivation (attrs: {
|
|
patches = [ ./patches/rpud.patch ];
|
|
CUDA_HOME = "${pkgs.cudatoolkit}";
|
|
});
|
|
|
|
WideLM = old.WideLM.overrideDerivation (attrs: {
|
|
patches = [ ./patches/WideLM.patch ];
|
|
configureFlags = [
|
|
"--with-cuda-home=${pkgs.cudatoolkit}"
|
|
];
|
|
});
|
|
|
|
EMCluster = old.EMCluster.overrideDerivation (attrs: {
|
|
patches = [ ./patches/EMCluster.patch ];
|
|
});
|
|
|
|
spMC = old.spMC.overrideDerivation (attrs: {
|
|
patches = [ ./patches/spMC.patch ];
|
|
});
|
|
|
|
BayesLogit = old.BayesLogit.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesLogit.patch ];
|
|
});
|
|
|
|
BayesBridge = old.BayesBridge.overrideDerivation (attrs: {
|
|
patches = [ ./patches/BayesBridge.patch ];
|
|
});
|
|
|
|
openssl = old.openssl.overrideDerivation (attrs: {
|
|
patches = [ ./patches/openssl.patch ];
|
|
OPENSSL_HOME = "${pkgs.openssl}";
|
|
});
|
|
|
|
Rserve = old.Rserve.overrideDerivation (attrs: {
|
|
patches = [ ./patches/Rserve.patch ];
|
|
configureFlags = [
|
|
"--with-server" "--with-client"
|
|
];
|
|
});
|
|
|
|
nloptr = old.nloptr.overrideDerivation (attrs: {
|
|
configureFlags = [
|
|
"--with-nlopt-cflags=-I${pkgs.nlopt}/include"
|
|
"--with-nlopt-libs='-L${pkgs.nlopt}/lib -lnlopt_cxx -lm'"
|
|
];
|
|
});
|
|
|
|
# Depends on broken ecespa package.
|
|
selectspm = old.selectspm.override { hydraPlatforms = stdenv.lib.platforms.none; };
|
|
|
|
# Depends on broken qtbase package.
|
|
qtutils = old.qtutils.override { hydraPlatforms = stdenv.lib.platforms.none; };
|
|
qtpaint = old.qtpaint.override { hydraPlatforms = stdenv.lib.platforms.none; };
|
|
bamboo = old.bamboo.override { hydraPlatforms = stdenv.lib.platforms.none; };
|
|
|
|
};
|
|
in
|
|
self
|